#!/bin/bash -e

function info() {
echo Usage: `basename $0` 'in.vcf'
exit 2
}

while getopts  ":p:f:" opt; do
	case  $opt  in
		p) out_prefix=$OPTARG;;
		f) suffix=$OPTARG;;
		*) info;;
	esac
done
shift $(($OPTIND - 1))


if [ $# -lt 1 ]; then info; fi

. $var

cat $1 |sed 1d|grep -F './.' > no_cov
cat $1 |sed 1d|grep -F -v './.' > cov
cat cov|grep -F '0/0' > ref
cat cov|grep -F -v '0/0' > all

wc -l $1 no_cov cov ref all > cov_stat